We have characterized the human and mouse S-antigens and 33K protein genes and a human Shuzin gene, and we have determined the gene sequences of the human and mouse S-antigens. The S-antigen genes were approximately 50 kbp in length, contained 16 exons and 15 introns, and comprised of 97% intron and 3% exon. The 5'-flanking regions of the genes, approximately 1.5 kbp long, had no known regulatory elements for transcription, such as TATA, GC, or CCAAT boxes. Interestingly, the 5' flanking regions of the human, bovine, and mouse genes expressed tissue-specific promoter activity in both in vitro and in vivo transcription assays as well as in transgenic mice. Isolation of two 33K protein genes and determination of their DNA sequences revealed genes of approximately 10 kbp in length, containing four exons and three introns. The 33K protein gene seems to represent a family of genes: At least three genes have similar sequences. The functional role of the retinal protein Shuzin is unknown. We isolated and sequenced several cDNAs each from humans and cows. The entire human Shuzin gene sequence also was determined. This gene, composed of two introns and three exons, has a highly repetitive sequence in the 5' noncoding region. We have constructed fusion genes containing a 5'-flanking S-antigen gene sequence upstream of the bacterial gene chloramphenicol acetyl transferase (CAT). A hybrid gene containing the 5'-flanking region of the mouse S-antigen gene and the CAT gene was microinjected into transgenic mice. The mice expressed CAT activity in the retina and pineal gland, suggesting that the 1,300 bp S-antigen promoter segment contains sufficient information to direct appropriate tissue-specific gene expression in transgenic mice. In addition, S-antigen was found in lens fiber and epithelial cells, the cerebellum, and the cerebral cortex. These results indicate that S-antigen is expressed in a wider spectrum of the cell types than previously recognized.